The aim of the proposed research is to understand the principles of specific molecular recognition that determine the structural stability and flexibility of oligonucleotide duplexes containing modified residues. These oligonucleotide analogs are intended to be antisense agents with nuclease resistance and high binding affinity for targeting gene sequences. DNA dimer synthons with achiral and neutral backbone linkages, such as peptide or thioformacetal linked dimers, and pyrimidine derivatives will be synthesized and incorporated into dodecamer sequences. The resulting oligonucleotide analogs will be studied in the context of DNA-DNA and hybrid DNA-RNA duplexes by using high resolution multidimensional NMR spectroscopy. By using well-characterized unmodified duplexes to set the basic scheme and then systematically introducing nucleotide analogs at designated sites, the chemistry, structural perturbation and conformational flexibility of modified oligonucleotide duplexes will be examined and compared. Various NMR parameters such as dipolar and scalar couplings and relaxation rates will be measured and analyzed in detail. The corresponding proton-proton distances and dihedral torsion angles will be utilized in modeling computations of oligonucleotide analogs for elucidation of three-dimensional structures. Such systematic and detailed structural information is presently not available for antisense duplexes. These results should provide insights into the effects of backbone or base modifications on local as well as global structure and dynamics of modified oligonucleotide duplexes. This study forms a basis for continuing research in predictive modeling of nucleotide analogs of potential therapeutic applications in gene regulation.